Dutch Society for Mass Spectrometry

Enhancing Tandem MS Sensitivity and Peptide Identification via Ion Preaccumulation in an Orbitrap Mass Spectrometer High-throughput mass spectrometry-based proteomics has gained increasing interest for both academic and industrial applications. As implementation of faster gradients has facilitated higher sample thr...

Boosting Orbitrap MS/MS speed to ∼70 Hz? 🚀

Read how we did it in our latest paper 👇

pubs.acs.org/doi/10.1021/...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

www.nature.com/articles/s41...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

We’re excited to announce the publication of Cascadia, our new de novo sequencing model designed for DIA data. By extending the transformer architecture to fully capture the complexities of DIA data, we achieve state-of-the-art performance.

www.nature.com/articles/s41...

Are you looking forward to attending #EuPA2025 in beautiful Saint-Malo? Get ready for an enriching experience in extraordinary #proteomics!

🗓️ Mark your calendar for the SCIEX lunch symposium, taking place on Wednesday, June 18!

🔗 Full show agenda 👉 bit.ly/3HcA6Hw

#SkepticsWelcome #ZenoTOF8600

Free structural MS hands-on workshop @ BIOCEV (CZ)

📅 Sept 15–19, 2025

For PhDs, postdocs & undergrads (CZ/SK)

HDX-MS, native MS, cross-linking, high-res MS, data processing

Apply by July 31 → bit.ly/3HNyzIg

@spidocs.bsky.social @mbuavcr.bsky.social @ciisbinstructcz.bsky.social

🌞Wishing everyone in the mass spec community a fantastic summer break!

Whether you are kicking back with the NVMS summer newsletter 👉 www.nvms.nl/index.php/nv... or diving into fresh data, wishing you sunshine, fun, and great results! 😄

#MassSpec #NVMS

Increased EThcD efficiency on the hybrid Orbitrap Excedion Pro Mass Analyzer extends the depth in identification and sequence coverage of HLA class I immunopeptidomes Gaining a complete and unbiased understanding of the non-tryptic peptide repertoire presented by HLA-I complexes by LC-MS/MS is indispensable for therapy design for cancer, autoimmunity and infectious...

We explored the Excedion Pro Mass Analyzer with faster & more efficient EThcD capabilities, launched @asms.org, to more efficiently convert MS2 spectra to PSMs, as quality & unambiguous identification are more important parameters than peptide numbers. www.biorxiv.org/content/10.1...

Couldn’t find and forgot to tag @lperezpaneda.bsky.social on this, she did awesome work analyzing the data!

Engineering Life 2025: ORIGIN AND FUNCTION OF MECHANICAL FORCES IN BIOLOGY Engineering Life 2025, biological forces, force spectroscopy, measuring forces, developmental forces, molecular motors, forces in morphogenesis, cytoskeleton, DNA mechanics, bionanotechnology

📢Conference alert📢

Only one week left to register for the Engineering Life 2025 Symposium at Dresden September 1-3. This year's edition focuses on the function of mechanical forces in biology.

engineering-life-dresden.de

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment www.nature.com/artic...

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#proteomics #prot-paper

🚨 Preprint alert 🚨 | Justin J.J. van der Hooft 🚨 Preprint alert 🚨 --> Large-scale unsupervised mass spectral discovery with improved annotation and customized searching by MS2LDA 2.0 Very proud of Laura Rosina Torres Ortega, Jonas Dietrich, a...

🚨 Preprint alert 🚨
--> Large-scale unsupervised mass spectral discovery with improved annotation and customized searching by MS2LDA 2.0

#metabolomics #CompMetabolomics #software #substructure #annotation #data #patterns #MolNetEnhancer #networking

www.linkedin.com/posts/jjjvan...

NVMS Spring Meeting 2025 - 1/3 📢
What a fantastic NVMS Spring Meeting at Sanquin Research in Amsterdam! The day was packed with cutting-edge mass spec talks, and a great atmosphere for networking. A big thank you to all speakers, attendees, and sponsors who made it such a success! 👍👏
www.nvms.nl

NVMS Spring Meeting 2025 - 2/3 📢
We were proud to see so many excellent talks from young researchers! Special congratulations to Alienke van Pijkeren (RUG) winner of the youngNVMS poster prize for her exciting work on single-cell proteomics. Great science and well-deserved recognition!👍👏
www.nvms.nl

NVMS Spring Meeting 2025 - 3/3 📢
At the General Assembly, we reviewed activities, and unanimously confirmed anoukrijs.bsky.social for a second term as NVMS Chair. Thank you, Anouk, for your continued dedication to the Dutch mass spec community!
📸 Don’t miss the full recap on our website: www.nvms.nl

🚨 NVMS Spring Meeting: Program Announced! 🚨
26th May 2025 | Sanquin, Amsterdam
The agenda is live – and the event is fully booked!
Still want to join? Check the program and add your name to the waiting list: www.nvms.nl/index.php/nv...

#NVMS #MassSpec

Excited to announce our revamped PhD-level BioMS course this September:

Advanced Proteomics for Drug Discovery and Biotherapeutics

Great line-up of instructors and topics, registration is open:
www.hecklab.com/advanced-pro...

Do-It-Yourself De Novo Antibody Sequencing Workflow that Achieves Complete Accuracy of the Variable Regions Antibodies are widely used as research tools or therapeutic agents. Knowing the sequences of the variable regions of an antibody─both the heavy chain and the light chain─is a prerequisite for the production of recombinant antibodies. Mass spectrometry-based de novo sequencing is a frequently used, and sometimes the only approach to gaining this information. Here, we describe a workflow that enables accurate sequence determination of monoclonal antibodies based on mass spectrometry data and freely available software tools. This workflow, which we developed using a homemade anti-FLAG monoclonal antibody as a reference sample, achieved 100% accuracy of the variable regions with clear distinction between leucine (L) and isoleucine (I). Using this workflow, we successfully decoded a monoclonal anti-HA antibody, for which we had no prior knowledge of its sequence. Based on the de novo sequencing result, we generated a recombinant anti-HA antibody, and demonstrated that it has the same specificity, sensitivity, and affinity as the commercial antibody.

Do-It-Yourself De Novo Antibody Sequencing Workflow that Achieves Complete Accuracy of the Variable Regions #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer Nature Communications - While DIA has advanced standard proteomics, its application in glycoproteomics has remained limited. Here, the authors present an optimized narrow-window DIA method for...

rdcu.be/ehinQ Read how a $1,- piece of cotton makes the difference for Shelley Jager enabling in-depth plasma N-glycoproteome profiling

📢Just 3 months to go until the 16th MaxQuant Summer School! #MQSS2025
Join us in Utrecht, Netherlands from July 21–25, 2025, for a week of in-depth training in mass-spectrometry-based proteomics.
Register now: eventbrite.de/e/maxquant-s...
#TeamMassSpec

The NVMS Spring Meeting at Sanquin, Amsterdam, on May 26th is almost here! 🌟

🔬 Abstract submission is still open for oral & poster presentations, send you abstract to: program@nvms.nl, deadline: April 7th

Registration link is on our website: www.nvms.nl

#NVMS #MassSpectrometry #Amsterdam #Sanquin

🌟We are excited to see you all at the NVMS Spring Meeting in Amsterdam on May 26th! Let’s make it a memorable event!😀

Stay tuned via our website: www.nvms.nl

The NVMS Spring Meeting at Sanquin, Amsterdam, on May 26th is almost here! 🌟

🔬 Abstract submission is still open for oral & poster presentations, send you abstract to: program@nvms.nl, deadline: April 7th

Registration link is on our website: www.nvms.nl

#NVMS #MassSpectrometry #Amsterdam #Sanquin

Some Bruker leaks for this year:
- New MS in development... a QQQ
- OmniTIMS advances (rolling out across multiple labs in Europe)
- New LC but doesn't look like a big advance over the nanoElute 2

Release DIA-NN 2.0 · vdemichev/DiaNN We are excited to announce DIA-NN 2.0, the most significant milestone in the history of DIA-NN development. Key Breakthroughs Proteoform Confidence mode: DIA-NN 2.0 solves the long-standing chall...

We have released DIA-NN 2.1.0, download link github.com/vdemichev/Di..., release notes github.com/vdemichev/Di....
It is a minor update, main highlights are:
- Built-in support for Thermo .raw (Windows + Linux)
- New QC metrics in PDF report & visualising trends across the experiment

Prolonged Trapping of Adeno-Associated Virus Capsids Reveals that Genome Packaging Affects Single-Ion Mass Spectrometry Measurements Recombinant adeno-associated viruses (rAAVs) play an important role in gene therapy, yet the optimal preparation of these biotherapeutics remains challenging, with often incomplete incorporation of genome cargo, negatively affecting therapeutic use. Genome packaging has traditionally been difficult to investigate. Charge detection mass spectrometry (CDMS) has gained prominence, as it provides the ability to mass analyze and resolve empty and filled rAAVs, enabling the quantitative determination of empty-to-filled rAAV ratios. Such measurements require a high mass resolving power and depend on the unbiased detectability of the distinct rAAV particles. The mass resolving power in the Orbitrap mass analyzers scales with transient recording times. Therefore, we extended the capability of recording ions from 1 or 2 to 24 s. When we record these 24 s transients to analyze rAAVs, we not only observe a substantial improvement in accuracy and mass resolution but also find that this can lead to erroneous artifacts in the empty-to-filled ratios. Artifacts originate from the distinct behavior between orbiting ions from either empty or filled particles, mainly due to differences in desolvation and charge losses. Ions from empty rAAVs appear much more susceptible to charge losses, which negatively affect their tracing, artificially decreasing the empty-to-filled ratios. Further elucidating the causes of this undesirable ion behavior, we provide the means to minimize charge losses, thus regaining accurate AAV quantification at an increased charge precision and mass-resolving power. As the Orbitrap-based CDMS has become a method of choice to determine this important quality control attribute, our findings are important to avoid reporting incorrect empty-to-filled ratios.

New work from Eduard and the @utrechtuniversity.bsky.social team in collaboration with ThermoFisher. Prolonged Trapping of Adeno-Associated Virus Capsids Reveals that Genome Packaging Affects Single-Ion Mass Spectrometry Measurements | pubs.acs.org/doi/10.1021/.... Be aware doing quantitative CDMS.

Lipidation of proteins has diverse essential roles in biology.

In his amazing keynote lecture at #Lunteren, Marc Baggelaar talked about his group's exciting contributions to better understand protein lipidations using #ChemicalProteomics. (1/5)
#chemsky #ChemBio

Prolonged Trapping of Adeno-Associated Virus Capsids Reveals that Genome Packaging Affects Single-Ion Mass Spectrometry Measurements Recombinant adeno-associated viruses (rAAVs) play an important role in gene therapy, yet the optimal preparation of these biotherapeutics remains challenging, with often incomplete incorporation of genome cargo, negatively affecting therapeutic use. Genome packaging has traditionally been difficult to investigate. Charge detection mass spectrometry (CDMS) has gained prominence, as it provides the ability to mass analyze and resolve empty and filled rAAVs, enabling the quantitative determination of empty-to-filled rAAV ratios. Such measurements require a high mass resolving power and depend on the unbiased detectability of the distinct rAAV particles. The mass resolving power in the Orbitrap mass analyzers scales with transient recording times. Therefore, we extended the capability of recording ions from 1 or 2 to 24 s. When we record these 24 s transients to analyze rAAVs, we not only observe a substantial improvement in accuracy and mass resolution but also find that this can lead to erroneous artifacts in the empty-to-filled ratios. Artifacts originate from the distinct behavior between orbiting ions from either empty or filled particles, mainly due to differences in desolvation and charge losses. Ions from empty rAAVs appear much more susceptible to charge losses, which negatively affect their tracing, artificially decreasing the empty-to-filled ratios. Further elucidating the causes of this undesirable ion behavior, we provide the means to minimize charge losses, thus regaining accurate AAV quantification at an increased charge precision and mass-resolving power. As the Orbitrap-based CDMS has become a method of choice to determine this important quality control attribute, our findings are important to avoid reporting incorrect empty-to-filled ratios.

Prolonged Trapping of Adeno-Associated Virus Capsids Reveals that Genome Packaging Affects Single-Ion Mass Spectrometry Measurements #JACS pubs.acs.org/doi/10.1021/...

The NVMS Conference Fund 2025 awardees are selected!
Congrats to:
🔹 Kevin Hooijschuur (Utrecht)
🔹 Raya (Arta) Sadighi (VU Amsterdam)
🔹 Laura Finazzi (Radboud)
🔹 Kimberly Garcia (Maastricht)
🔹 Kas Houthuijs (VU Amsterdam)
They’ll represent Dutch Mass Spec at international events this year! 🌍✨ #NVMS

Excited to be giving this webinar soon. Hope to see you then!

In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer Nature Communications - While DIA has advanced standard proteomics, its application in glycoproteomics has remained limited. Here, the authors present an optimized narrow-window DIA method for...

Just out by Shelley Jager: rdcu.be/edEnO. One of the fastest & deepest plasma glycoproteomics studies. Take home message; we even detect glycosylated cytokines and chemokines, but also still need better software. #glycotime @utrechtuniversity.bsky.social @bijvoet-centre.bsky.social